It's extremely popular in stories to have your protagonist have parents divorced, one parent dead, both parents dead, etc. It's not just a staple of anime, it's a staple of story telling. How many characters do you know that have both parents and both parents are alive and together, regardless of whether they show up on screen.

I'll start

Surprisingly:

Even though his father is often away on business, his parents are both alive and together. Hell his grandparents are both alive and together. It's extremely rare for this type of story. Especially considering that Jonathan only had his dad, George (Jonathan's son only had his mother), and Joseph only had his grandmother at first, and then later met his mother. Jotaro was lucky, he grew up knowing both of his parents and both of his grandparents.